Metagenomics to Bioremediation: Applications, Cutting Edge Tools, and Future Outlook

Front Cover
Metagenomics to Bioremediation
Copyright
Dedication
Contents
Contributors
About the editors
Acknowledgments
Section 1: Introduction to bioremediation and metagenomics
Chapter 1: Bioremediation: A green technology for environmental cleanup
1. Introduction
2. Agents of bioremediation
2.1. Bioremediation by bacteria
2.2. Bioremediation by fungus
2.3. Bioremediation by algae
3. Role of biotechnology in bioremediation
4. Microorganisms to clean up contaminated environments
4.1. The role of microbes in bioremediation
4.2. How microbes destroy contaminants
4.3. Pollutants that are biodegradable
4.3.1. Hydrocarbons
4.3.2. Polycyclic aromatic hydrocarbons (PAHs)
4.3.3. Polychlorinated biphenyls (PCBs)
4.3.4. Pesticides
4.3.5. Dyes
4.3.6. Radionuclides
4.3.7. Heavy metals
5. Bacterial degradation
5.1. PGPR and PGPB degradation
5.2. Microfungi and mycorrhiza degradation
5.3. Yeasts degradation
6. Degradative capacities of algae and protozoa
7. Plant-assisted bioremediation
7.1. Mechanism of phytoremediation of contaminated soils
7.1.1. Phytoextraction (phytoaccumulation of contaminants)
7.1.2. Phytostabilization (immobilization of contaminants)
7.1.3. Phytovolatilization (evapotranspiration of detoxified contaminants)
7.1.4. Rhizofiltration
7.1.5. Phytostimulation (microbe stimulated phytoremediation)
8. Mycorrhiza assisted phytoremediation
9. Limitations of bioremediation
10. Conclusion
Chapter 2: Recent trends in bioremediation of heavy metals
1. Introduction
2. Heavy metals: Sources and environmental effects
3. Effect of heavy metal toxicity on soil, microorganisms, and plants
4. Heavy metals toxicity in human beings
5. Bioremediation and its significance
5.1. The need for bioremediation: Demerits of conventional remediation methods
5.2. What is bioremediation?
5.3. Phytoremediation
5.4. Bioremediation with algae
5.5. Microbial bioremediation
5.5.1. Bacterial bioremediation
5.5.2. Fungal bioremediation
6. Metagenomics and its application in bioremediation
6.1. Metagenomics methodology
6.2. Application of metagenomics for the remediation of different contaminated mediums
7. Conclusion
Chapter 3: Recent advances in bioremediation by metagenomics-based approach for pharmaceutical derived pollutants
1. Introduction
2. Bioremediation
2.1. Bioremediation methods involved in purifying air pollutants
2.2. Bioremediation in the removal of water pollutants
3. Bioremediation techniques
3.1. Ex situ bioremediation technologies
3.1.1. Biopile
3.1.2. Windows
3.1.3. Bioreactor
3.1.4. Land farming
3.2. In situ bioremediation techniques
3.2.1. Bioventing
3.2.2. Biosparging
3.2.3. Phytoremediation
3.2.4. Permeable reactive barrier (PRB)
3.2.5. Intrinsic bioremediation
4. Pharmaceutical wastes
4.1. Different types of pharmaceutical wastes
4.1.1. Over-the-counter drug wastes
4.1.2. Non-hazardous drug wastes
4.1.3. Hazardous drug wastes
5. Controlled drug wastes
5.1. Pharmaceuticals for veterinary use
5.2. Agricultural use of pharmaceutical
5.3. Sources of pharmaceutical waste products
5.3.1. Pharmaceutical manufacturing plants
5.3.2. Health care institution and extended care facilities
5.3.3. Personal care product (PCPs) manufacturers
5.4. Veterinary offices
6. Regulation of the disposal of pharmaceutical wastes
7. Characteristic hazardous wastes
8. Remediation methods for pharmaceutical waste
8.1. How bioremediation process helps in remediating pharmaceutical wastes?
8.2. Bioremediation of pharmaceutical wastes using cow dung/gomeya
8.2.1. Composition of cow dung/gomeya
8.3. Bioremediation of pharmaceuticals and pesticides
8.3.1. Antimicrobial agents
8.3.2. Degradation of biomedical waste by bioremediation process
8.3.3. Bioremediation of pesticides using cow dung
8.4. Mycoremediation: A process to remediate pharmaceutical wastes
8.5. Green approaches
9. Conclusion
Chapter 4: Metagenomics in bioremediation: Recent advances, challenges, and perspectives
1. Introduction
2. Microorganisms that are important in biosorption
3. Omics approach in bioremediation/biosorption
4. Application of metagenomics in bioremediation
5. Exploring microbial communities using next-generation sequencing
5.1. Shotgun sequencing
5.2. Sanger sequencing
5.2.1. Short-read sequencing
5.2.2. Long-read (third-generation) sequencing
5.2.3. 16S rRNA amplicon sequencing
6. Molecular biology approach in bioremediation
6.1. 16S rRNA and other specific gene approaches
6.2. PCR, RT-PCR, and qPCR technologies
6.3. Temperature or denaturing gradient gel electrophoresis
6.4. Amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis
6.5. Terminal-restriction fragment length polymorphism (T-RFLP)
6.6. Fluorescent in situ hybridization (FISH)
6.7. Applications of DNA microarray technologies
6.8. Nucleic acids based stable isotope probing (SIP)
6.9. Compound-specific isotope analysis (CSIA)
7. Role of transcriptomics and metatranscriptomics in bioremediation
8. Conclusion and future direction
Chapter 5: Metagenomic approaches for understanding microbial communities in contaminated environments: Bioinformatic too ...
1. Introduction
2. Sequencing-based study of environmental microbiomes
2.1. Metataxonomics or amplicon sequence-based microbiome surveys
2.2. Metagenomics
2.3. Metatranscriptomics
3. Bioinformatic analysis of high-throughput sequencing data
3.1. Quality control
3.2. 16S rRNA data analysis
3.3. Metagenomic classification
3.4. Metagenomic assembly
3.5. Binning and MAGs
3.6. Strain level metagenomic analysis
3.7. Assembly pipelines
3.8. Metatranscriptomic analysis
3.9. Integrated metatranscriptomic workflows
4. Microbial community structure and processes in contaminated environments
4.1. Petroleum hydrocarbons
4.2. Acid mine drainage
4.3. Radioactive waste
4.4. Pesticides and herbicides
4.5. Azo dyes
4.6. Industrial wastewaters
5. Challenges and future outlook
6. Conclusions
Chapter 6: Microbial enzymes and their budding roles in bioremediation: Foreseen tool for combating environmental pollution
1. Introduction
2. Pollutants: The stubborn enemy
2.1. Heavy metals
2.1.1. Arsenic
2.1.2. Lead
2.1.3. Mercury
2.1.4. Chromium
2.2. Persistent organic pollutants (POPs)
2.3. Petroleum products
2.4. Radioactive isotopes
3. Bioremediation
3.1. Classification of bioremediation
3.1.1. In situ bioremediation
3.1.2. Ex situ bioremediation
3.2. Types of bioremediation
3.2.1. Bio-stimulation
3.2.2. Bio-augmentation
3.2.3. Mycoremediation
3.2.4. Enzymatic remediation
4. Microbial enzymes in bioremediation
4.1. Oxidoreductases
4.1.1. Oxygenases
Mono-oxygenases
Dioxygenases
4.1.2. Laccases
4.1.3. Peroxidases
Lignin peroxidase (LiP)
Manganese peroxidase (MnP)
Versatile peroxidase
4.2. Hydrolases
4.2.1. Lipases
4.2.2. Cellulase
4.2.3. Protease
4.2.4. Carboxylesterases
4.2.5. Phosphotriesterases
4.2.6. Dehalogenases
5. Molecular advancements in bioremediation
5.1. Genetic engineering
5.2. Enzyme engineering
5.3. Enzyme immobilization
5.4. Nanozymes
6. Conclusion and future prospects
Acknowledgments
Chapter 7: Interface of `meta-omics in gut biome remediation to unravel the complications of environmental pollutants
1. Introduction
2. Environmental pollution-A rising social menace
3. Crucial transformations of pollutants as toxicants
4. Intrusions into the human system as various ailments
5. Beneficial microbial ecosystems-Overview
6. Gut biome as potential bio remediators to transformer toxicants
7. Biosorption of toxicants in the human body-The interplay of gastrointestinal (GI) microbiotas
8. Vital microbial metabolites and their mechanism in bioremediation targeting various environmental pollutants
9. The metabolization of gut microbiota on various environmental chemicals
9.1. Heavy metals
9.2. Pesticides
9.3. Plastics
10. Meta-omics, the tool to bridge host-microbe interactions
10.1. Metagenomics
10.2. Metatranscriptomics
10.3. Metaproteomics
10.4. Metabolomics
11. Metabolic modeling
12. Computational approaches to investigate the microbiome
13. Applications of GEM in gut bioremediation
14. Conclusion
Section 2: Bioremediation and metagenomics in environmental remediation
Chapter 8: Bioremediation: A favorable perspective to eliminate heavy metals from polluted soil
1. Heavy metal pollution and bioremediation
2. Types of bioremediation
3. Importance and applications of bioremediation
4. Heavy metals in soil pollution
5. Bioremediation of heavy metals
5.1. Bacterial bioremediation of cadmium (Cd)
5.2. Fungal bioremediation of cadmium
5.3. Phytoremediation of cadmium
5.4. Bacterial bioremediation of mercury (Hg)
5.5. Fungal bioremediation of mercury
5.6. Phytoremediation of mercury
5.7. Bacterial bioremediation of lead (Pb)
5.8. Fungal bioremediation of lead
5.9. Phytoremediation of lead
5.10. Chromium (Cr)
5.10.1. Bioremediation of chromium
5.10.2. Bacterial bioremediation of chromium
5.10.3. Fungal bioremediation of chromium
5.10.4. Phytoremediation of chromium
5.11. Bioremediation of arsenic (As)
5.11.1. Bacterial bioremediation of arsenic
5.11.2. Fungal bioremediation of arsenic
5.11.3. Phytoremediation of arsenic
6. Conclusion
Chapter 9: Metagenomics in bioremediation of metals for environmental cleanup
1. Introduction
2. Metals and metal toxicity
3. Metal pollution
3.1. Sources of metal pollution
3.1.1. Anthropogenic sources
3.1.2. Natural sources of metal pollution
3.2. Challenges of environmental cleanup of metal pollution
4. Bioremediation of metals
4.1. Microbial adaptations exploited in metal bioremediation
4.1.1. Biosorption
4.1.2. Oxidation/reduction of metals
4.1.3. Siderophores
4.1.4. Biosurfactants
4.1.5. Biofilms
4.1.6. Metallothiones
4.2. Methods for bioremediation of metals
5. Metagenomics for microbiome analysis
5.1. Metagenomes of a healthy environment
5.2. Metagenome of metal pollution
5.3. Implications of the metagenome in bioremediation of metal
6. Environmental sampling for metagenome analysis
7. Sequencing technologies for metagenome analysis
7.1. Second-generation sequencing
7.1.1. Roche 454 pyrosequencing
7.1.2. Ion torrent sequencing
7.1.3. Illumina Solexa sequencing
7.2. Third-generation sequencing
7.2.1. Oxford Nanopore sequencing
7.2.2. PacBio sequencing
7.2.3. Sequence quality
7.3. Targeted gene sequencing
7.4. Shot gun metagenomics
7.4.1. Assembly
7.5. Technologies for functional and pathway analysis
Chapter 10: Microbial community and their role in bioremediation of polluted e-waste sites
1. Introduction
2. E-waste the current scenario
3. Microbes thriving in E-waste contaminated site
3.1. Culture independent study
3.2. Culture dependent study
4. Bioremediation of E-waste
4.1. Bioleaching
4.2. Biosorption
4.3. Bioreduction of metals
4.4. Biomineralization
4.5. Bioremediation of organic pollutants of E-waste
5. Challenges and future opportunities
6. Conclusion
Chapter 11: Metagenomic analysis of wastewater for water quality assessment
1. Introduction
2. Natural microbiome of water
3. Metagenomic analysis of wastewater
3.1. The metagenome analysis of residential wastewater for bioremediation
3.2. Metagenome analysis of agricultural wastewater for bioremediation
3.3. Metagenome analysis of industrial wastewater for bioremediation
3.4. Metagenome analysis of hospital effluent for bioremediation
4. Impact of wastewater treatment on microbial composition
5. Molecular techniques for analysis of microbial communities in wastewater
5.1. Fingerprint techniques for metagenomic analysis of wastewater
5.1.1. Gradient gel electrophoresis
5.1.2. Random amplification of polymorphic DNA (RAPD)
5.1.3. Terminal restriction fragment length polymorphism (T-RFLP)
5.1.4. Ribosomal intergenic spacer analysis (RISA)
5.1.5. Single-strand conformation polymorphism (SSCP)
5.2. Hybridizing techniques for microbial detection
5.2.1. Microarray
5.2.2. Fluorescent in situ hybridization (FISH)
5.2.3. Quantitative PCR (qPCR)
6. Metagenomic approaches for wastewater analysis and bioremediation of wastewater
6.1. Wastewater sampling for metagenome analysis
6.2. Tools for metagenomic analysis of wastewater and bioremediation of wastewater
6.2.1. DNA sequencing for taxonomic classification
6.2.2. Marker gene analysis
6.2.3. Clone library
6.2.4. Second-generation sequencing
454 Pyrosequencing
Ion torrent
Illumina
6.2.5. Whole metagenome sequencing
6.2.6. Shotgun metagenome sequencing
6.2.7. Third generation sequencing
7. Antibiotic resistance genes in wastewater
8. Metagenomic analysis to assess metabolic pathways in bioremediation
9. Limitations of metagenomics in wastewater treatments
Chapter 12: The proteome mapping-Metabolic modeling, and functional elucidation of the microbiome in the remediation of d ...
1. Introduction
2. Elucidation of the microbiome in situ
2.1. Metaproteomics-The near future
2.2. Proteogenomics-The difference and significance
3. Computational efficacy in metaproteomic studies
4. Metabolic engineering and microbial ecology
5. Present and future of microbiome research
5.1. Wastewater treatment and activated sludge
5.2. Acid mine drainage (AMD)
5.3. Dye remediation
5.4. Environmental stress response
5.5. Bioremediation of environmental xenobiotics and industrial effluents
6. Challenges of metaproteomics and future prospects
Chapter 13: Wastewater treatment processes and microbial community
1. Introduction
1.1. What is wastewater?
1.2. Types of wastewater
1.3. Harmful effects of wastewater
2. Wastewater treatment processes
2.1. Physical wastewater treatment
2.1.1. Screening
2.1.2. Grit removal
2.1.3. Sedimentation
2.1.4. Filtration
2.2. Chemical wastewater treatment
2.2.1. Coagulation and flocculation
2.2.2. Ozonation
2.2.3. Chlorination
2.2.4. Activated carbon
2.3. Biological treatment
2.3.1. Microorganisms
2.3.2. Suspended growth biological treatment
2.3.3. Attached growth process
2.3.4. Enhanced biological phosphorus removal
2.3.5. Nitrification and denitrification
2.4. Non-conventional microbial wastewater treatment
2.4.1. Microbial electrolysis cell (MEC)
2.4.2. Microbial fuel cell (MFC)
3. Conclusions
Chapter 14: Water quality and wastewater treatment for human health and environmental safety
1. Introduction
2. Industrial wastewater
3. Domestic wastewater
4. Agricultural wastewater
5. Environmental and health impact of wastewater discharge into water resources
6. Parameters to assess water quality
6.1. Chemical parameter
6.2. Physical parameters
6.3. Microbiological parameters
7. Wastewater treatment techniques
7.1. Primary stage
7.2. Secondary stage
7.3. Tertiary stage
8. Different processes in wastewater treatment
8.1. Physical processes in wastewater treatment
8.2. Chemical processes in wastewater treatment
8.3. Biological processes in wastewater treatment
8.4. Physicochemical treatment of wastewater
9. New trends in wastewater treatment
9.1. Nanotechnology in wastewater treatment
9.2. Advances in biofilm technology
9.3. Aerobic granulation technology
9.4. Microbial fuel cell technology
10. New trends in wastewater treatment
10.1. Satellite system for wastewater treatment
10.2. Use of computational fluid dynamics in wastewater treatment
10.3. Computational artificial intelligence in wastewater treatment
10.4. Geographical information system and satellite technology for wastewater treatment
Chapter 15: Bioremediation of petrochemical sludge from soils
1. Introduction
2. Characteristic properties of petroleum pollutants & toxicity of oil-polluted soil
3. Remediation processes of petroleum-polluted soil
4. Bioremediation technologies
4.1. Bioaugmentation
4.2. Biostimulation
4.3. Integrated methods
5. Conclusions and perspectives
Chapter 16: Bioremediation of nuclear waste effluent using different communities of microbes
1. Introduction
2. Bioremediation
3. Metagenomics in bioremediation
4. Overview of radionucleotides
4.1. Importance of radionuclides
4.2. Importance of radioactivity by radionuclides
5. Importance of microbial bioremediation
5.1. Clay-based buffer for microorganisms
5.2. Sulfate reducing bacteria in bioremediation
5.2.1. Reduction mechanism of Tc and uranium
5.3. Conventional methods of bioremediation
5.3.1. In situ bioremediation
5.3.2. Bioaccumulation to biotransformation process
6. Radioactive elements
6.1. Uranium
6.2. Neptunium
6.3. Plutonium
6.4. Americium
6.5. Technetium
6.6. Cesium
6.7. Strontium
7. Radionucleotides sources
7.1. Naturally occurring radioactive material
7.2. Nuclear fuel cycle
7.3. Medical source
7.4. Industrial waste
7.5. Levels of nuclear waste from power plants
7.6. Low-level radioactive waste
7.7. Disposal method for LLW
7.8. Intermediate level radioactive waste
7.9. Disposal method for ILW
7.10. High-level radioactive waste
7.11. Disposal method for HLW
8. Effects of radionucleotides
8.1. Biofilms
8.1.1. Organisms producing biofilms
8.2. Bacterium interactions with radionucleotides
8.2.1. Cyanobacteria in bioremediation
8.2.2. Archaea interaction with radionucleotides
8.2.3. Fungi interaction with radionucleotides
8.2.4. Algae interaction with radionucleotides
9. Conclusion
Chapter 17: Metagenomics of contaminated wetland sediment in a tropical region
1. Introduction
2. Application of ``omics´´ in natural/constructed wetlands
3. Metagenomic study in natural wetlands of Indian tropical region
4. Bacterial diversity in the rhizosphere of wetland plant T. latifolia L
5. Conclusion
Chapter 18: Hydrocarbons and environmental pollution: Metagenomics application as a key tool for bioremediation
1. Introduction
2. Hydrocarbons and their problems
2.1. Aliphatic and monoaromatic hydrocarbons
2.2. Polycyclic aromatic hydrocarbon
3. Application of microorganisms in bioremediation
4. Metagenomics
5. Conclusions
Chapter 19: A complete review on anaerobes and nanoparticles in wastewater treatment
1. Introduction
2. Biological wastewater treatment methods
2.1. Anaerobic digestion (AD) method
2.2. Up flow anaerobic sludge blanket reactor (UASB technology)
2.3. Anaerobic fluidized bed reactor
2.4. Fixed film reactor
2.5. Constraints of large-scale AD adaptation
2.6. AD's future application prospects
2.7. Inhibiting factors of AD
2.8. Effect of temperature
2.9. Effect of pH and nutrients
3. Bacterial communities involved in WWT
3.1. Coliforms (e.g., Escherichia coli)
3.2. Cyanobacteria (e.g., Oscillatoria)
3.3. Acetogenic bacteria (e.g., Acetobacter)
3.4. Nitrogen removal
3.4.1. Gram-negative anaerobic bacteria (e.g., E.coli)
3.4.2. Methane-forming bacteria (e.g., Methanobacterium)
3.4.3. Floc-forming bacteria (e.g., Sheathed bacteria)
3.4.4. Sludge thickening and filamentous growth
3.4.5. Gliding bacteria (e.g., Begglatoa)
3.4.6. Gram-negative, aerobic cocci and rods (e.g., Acetobacter)
3.4.7. Hydrolytic bacteria (e.g., Bacteriodes)
3.4.8. Nocardioforms (e.g., Nocardia)
3.4.9. Pathogenic bacteria (e.g., Camplyobacter)
3.4.10. Poly-P bacteria (e.g., Acinobacter)
Getting rid of phosphorus
3.4.11. Saprophytic bacteria (e.g., Micrococcus)
3.5. Microbial genomics in wastewater
4. Bio-augmentation
4.1. Septage in bioremediation
4.2. Methods available for the disposal of Septage
4.3. Significant components in domestic wastewater and septage
5. Membrane bio-engineering
5.1. Membrane technology implications
5.1.1. Microfiltration (MF)
5.1.2. Membrane bioreactors
5.1.3. Forward and reverse osmosis
6. Environmental ramifications of anaerobic (bio) sewage treatment
6.1. Climate resilience
6.2. Water protection
6.3. Resource conservation
7. Nanoparticle's technology
7.1. Metal nanoparticles
7.1.1. Immobilized TiO2 nanoparticles
7.1.2. Magnetic Ni nanoparticles
7.1.3. Fe nanoparticles
7.2. Nanoflowers
7.2.1. Ni nanoflowers
7.2.2. Green synthesis of ZnO nano-flowers
7.2.3. Zinc oxide nanoflowers
8. Conclusion
Section 3: Plant microbes association in environmetal remediation
Chapter 20: Metagenomic approach role of psychrotrophic and psychrophilic microbes in bioremediation
1. Introduction
2. Metagenomics of psychrotrophic microorganisms
3. Metagenomics of psychrophilic microorganisms
4. Bioremediation using psychrotrophic and psychrophilic microorganisms
5. Psychrotrophic and psychrophilic species of microorganisms used in bioremediation
6. Metagenomics in bioremediation using psychrotrophic and psychrophilic microorganisms
7. Metagenomic approach to hydrocarbon bioremediation (in aquatic environments) by psychrotrophic and psychrophilic micro ...
8. Drawbacks and future challenges of metagenomics of psychrophilic and psychrotrophic microorganisms
Chapter 21: Nano- and phytoremediation technique for textile wastewater treatment and successive production of fertilizers
1. Introduction
2. Textile dyes characteristics
3. Textile dyes classification
4. Influence of textile wastewater on environment
5. Potential pollutants in textile wastewater
5.1. Dyes
5.2. Dissolved solids
5.3. Suspended solids
5.4. Heavy metals
6. Environmental and health impacts of textile wastewaters
7. Bio-remediation techniques
7.1. Pure cultures
8. Nano-remediation
9. Phyto-remediation
10. Synergistic strategies for degradation of textile dyes and effluents
11. Reactor development and constructed wetland strategies for phytoremediation of textile dyes and effluents
12. Plant mechanisms for treatment of textile dyes and effluents
12.1. Adsorptive degradation of dyes
13. Factors affecting phytoremediation
13.1. Plant's growth form
13.2. Dye concentration and hydraulics
13.3. Oxygen, water, and nutrient availability
13.4. Temperature
13.5. Solar energy and radiations
14. Conclusion and futuristic approach
Acknowledgments
Chapter 22: Plant-microbes association: Psychrophilic and psychrotrophic microorganisms associated with plants and their ...
1. Introduction
2. Plant-psychrotrophic microorganism interactions
3. Plant-psychrophilic microorganism interactions
4. Environmental services of psychrotrophic and psychrophilic bacteria associated with plants
4.1. Biodegradation of contaminant compounds in cold climates
4.2. Bioinoculants to stimulate plant growth in cold climates
4.3. Bioinoculants that improve plant tolerance to low temperatures
4.4. Agents for biodegradation of agricultural residues at low temperatures
4.4.1. Energy generation from low-temperature biodegradation of agricultural wastes
4.4.2. Biodegradación de desechos agrícolas a bajas temperaturas para la producción de compost
Use and application of psychrotrophic and psychrophilic bacteria: Limitations and perspectives
Chapter 23: Metal-organic frameworks-based emerging platforms for recognition and monitoring of environmentally hazardous ...
1. Introduction
2. Potential applications of electrochemical sensors based on MOF for the sensing of organic pollutants
2.1. Detection of pesticides through MOF based sensors
2.2. Detection of antibiotics through MOF-based electrochemical sensors
2.3. Detection of phenolic compounds through MOF-based electrochemical sensors
3. Conclusion and future prospects
Chapter 24: Bioaugmentation of metal phytoremediation through plant-microbe interaction
1. Introduction
2. Biological availability of metals in soil
3. Metal hyperaccumulator plants
4. Limitations of hyperaccumulator plants
5. Using the rhizobiome to enhance hyperaccumulator competency
5.1. Rhizobacteria
5.2. Endophytes
6. Rhizobiome attributes that are advantageous for metal hyperaccumulators
6.1. Plant growth promotion (PGP) characteristics
6.1.1. Phytohormones
6.1.2. Nutrient acquisition
6.1.3. Escalating metal solubility by root exudates
6.1.4. Rhizobiome with metal-resistant characteristics
7. Application of plant growth-promoting rhizobacteria in mitigation of metal stress in plants
8. Endophytic bacteria versus rhizobacteria in alleviating metal stress
9. Other applications of PGPB
10. Conclusions and future research aspects
Section 4: Emerging green technologies in bioremediation and metagenomics
Chapter 25: Lignin-based hybrid materials in wastewater cleanup
1. Lignin
1.1. Types of lignin
1.1.1. Native lignin
1.1.2. Technical/commercialized lignin
1.2. Extraction methods of lignin
1.2.1. Kraft process
1.2.2. Soda process
1.2.3. Lignosulfonate process
1.2.4. Organosolv process
1.2.5. Enzymatic hydrolysis process
2. Modification in lignin
2.1. Synthesis of new chemically active sites
2.1.1. Amination
2.1.2. Nitration
2.1.3. Sulfomethylation
2.2. Conventional lignin modification
2.2.1. Alkylation
2.2.2. Esterification
2.2.3. Etherification
2.2.4. Urethanization
2.3. Lignin-based nanohybrids
2.3.1. Metal oxide-lignin hybrids
2.3.2. Metal-lignin hybrids
2.3.3. Carbon-lignin hybrids
2.3.4. Biobased nanoparticles-lignin hybrids
2.3.4.1. Coated lignin nanoparticles (CLN)
2.3.4.2. Lignocellulosic nanoparticles
3. Applications of lignin
3.1. Lignin-based adsorbents
3.1.1. Adsorption of metal ions
3.1.2. Adsorption of emerging pollutants
3.2. Lignin-based photocatalysts
3.3. Lignin-based bactericidal
3.4. Lignin-based flocculant
4. Conclusions
Acknowledgments
Chapter 26: Immobilized enzyme reactors for bioremediation
1. Introduction
2. Types of enzymes
3. Enzyme immobilization techniques
4. Immobilized enzyme reactors-recent advancements
5. Pros and cons of immobilized enzyme reactors
6. Immobilized enzyme reactor for wastewater treatment
7. Future perspectives
Acknowledgment
Chapter 27: Biochar processing for green and sustainable remediation: Wastewater treatment, bioenergy, and future perspective
1. Introduction
2. Biomass conversion techniques
2.1. Combustion
2.2. Gasification
2.3. Pyrolysis
2.3.1. Types
3. Effects of process parameters on biochar yield
3.1. pH
3.2. Effect of temperature
3.3. Residence time
3.4. Effect of particle size
3.5. Effect of biomass composition
4. Adsorption mechanism for aqueous contaminant removal
4.1. Organic pollutants
4.2. Heavy metals
4.3. Nitrogen and phosphorous removal
5. Application in wastewater treatment
5.1. Industrial wastewater treatment
5.2. Municipal wastewater treatment
5.3. Agricultural wastewater treatment
5.4. Stormwater treatment
6. Bioenergy production
6.1. Biodiesel production
6.2. Catalytic esterification
7. Future perspective: Concept of nano-biochar
Acknowledgments
Chapter 28: High-throughput sequencing technologies in metagenomics
1. Introduction
2. Current high throughput sequencing technology
3. Various commercially available second-generation platforms for metagenomic studies
3.1. Illumina platforms
3.2. BGI sequencing platform
3.3. Thermo fisher ion torrent platform
4. Various commercially available third-generation platforms for metagenomic research
4.1. PacBio's platform
4.2. Oxford nanopore technologies
4.3. Sample processing and library preparation
5. Data analysis
5.1. Raw data
5.2. Clean data
5.3. Human host subtraction
5.4. Reference databases
5.5. Taxonomic classification
5.6. Report
6. Challenges and future directions
6.1. Human host background
6.2. Intracellular bacteria and fungi
6.3. RNA instability in the process
6.4. Biological information analysis: Optimization of microbial databases and virus classification
6.5. Interpretation
6.6. Flaws in mNGS as compared to conventional approaches for microbe detection
7. Applications
7.1. Identification of antibiotic resistance genes
7.2. Characterization of the human microbiome
7.3. Gut microbiome dysbiosis and phenotype
7.4. Categorization of microbiome under specific conditions
7.5. Investigation of human host responses
7.6. Infectious disease diagnosis
8. Conclusion
Chapter 29: Genetically engineered microbes for bioremediation and phytoremediation of contaminated environment
1. Introduction
1.1. Bioremediation mechanisms using genetically modified microbes
1.2. Genetically modified microbes for bioremediation
1.3. Bioremediation of heavy metals
1.3.1. Remediation of mercury (Hg)
1.3.2. Remediation of cadmium
1.3.3. Remediation of arsenic
1.3.4. Nickel remediation
1.4. Bioremediation of oil spill
1.4.1. Genetically engineered microbial bioremediation for oil spill
1.5. Phytoremediation using genetically modified plants
1.5.1. Remediation of toxic explosive using transgenic plants
1.5.2. Remediation of heavy metals using transgenic plants
1.6. Advantages of genetically engineered microorganisms in bioremediation
2. Conclusion
Chapter 30: Proteomics monitoring of microbes in contaminated environments
1. Introduction
2. Techniques for metaproteomic studies
3. Fundamental developments of MS-based proteomics
4. Microbial community proteomics in different environments
4.1. Marine and freshwater metaproteomics
4.2. Soil metaproteomics
4.3. Wastewater and activated sludge metaproteomics
4.4. Acid mine drainage (AMD) biofilm metaproteomics
5. Challenges
6. Perspectives
7. Conclusion
Chapter 31: Development of biosensors for application in industrial biotechnology
1. Introduction
2. Development of biosensor
2.1. Biological receptor
2.2. Transducer
2.3. Working principle of biosensor
3. Application of biosensors in industrial biotechnology
3.1. Biosensor in food industry
3.2. Biosensors in cancer research
3.3. Smart packaging by biosensors
3.4. Role of biosensors in tissue engineering and its applications
3.4.1. Biosensing small molecules
3.4.2. Sensing of functional protein molecules
3.4.3. Analyte's detection
3.5. Environmental application of biosensors
3.5.1. Polychlorinated biphenyls (PCBs)
3.5.2. Heavy metals
3.5.3. Pesticides
3.5.4. Nitrogenous compounds and microbial detection
3.5.5. BODs
4. Latest advancement in biosensors
5. Conclusion
Chapter 32: Microbial enzymes: Versatile tools for pollution abatement
1. Introduction
2. Global scenario of pollution generation and possible remediation
2.1. Major pollutants
2.2. Remediation strategies: Multi-omics approach
3. Microbial enzymes and their coding genes: Multi-omics in bioremediation of major pollutants
3.1. Industrial pollutants
3.2. Agricultural pollutants
3.3. Plastic pollutants
3.4. Other pollutants
4. Enzyme-based smart technologies
4.1. Biosensors
4.2. Nanozymes
5. Future prospects and conclusion
Acknowledgment
Index
Back Cover